Development of a duplex real-time PCR for the detection of Rickettsia spp. and typhus group rickettsia in clinical samples

Diversity of Rickettsia species in collected ticks from Southeast Iran

Rickettsia occurs worldwide and rickettsiosis is recognized as an emerging infection in several parts of the world. Ticks are reservoir hosts for pathogenic Rickettsia species in humans and domestic animals. Most pathogenic Rickettsia species belong to the spotted Fever Group (SFG). This study aimed to identify and diagnose tick fauna and investigate the prevalence of Rickettsia spp. in ticks collected from domestic animals and dogs in the rural regions of Kerman Province, Southeast Iran. In this study, tick species (fauna) were identified and 2100 ticks (350 pooled samples) from two genera and species including Rhipicephalus linnaei (1128) and Hyalomma deteritum (972) were tested to detect Rickettsia genus using Real-time PCR. The presence of the Rickettsia genus was observed in 24.9% (95%CI 20.28-29.52) of the pooled samples. Sequencing and phylogenetic analyses revealed the presence of Rickettsia aeschlimannii (48.98%), Rickettsia conorii israelensis (28.57%), Rickettsia sibirica (20.41%), and Rickettsia helvetica (2.04%) in the positive samples. The results showed a significant association between county variables and the following variables: tick spp. (p < 0.001), Rickettsia genus infection in ticks (p < 0.001) and Rickettsia spp. (p < 0.001). In addition, there was a significant association between tick species and host animals (dogs and domestic animals) (p < 0.001), Rickettsia spp infection in ticks (p < 0.001), and Rickettsia spp. (p < 0.001). This study indicates a high prevalence of Rickettsia spp. (SFG) in ticks of domestic animals and dogs in rural areas of Kerman Province. The health system should be informed of the possibility of rickettsiosis and the circulating species of Rickettsia in these areas.

Detection of Various Rickettsial Species in Ticks Collected from Small Ruminants in Western Iran

Background: Most of the rickettsioses are transmitted by ticks, and often overlooked by the medical profession, but are clinically important as they cause major human diseases. Recent studies have shown the existence of some rickettsial species in Iran, but very little information is available about the status of rickettsial epidemiology and ecology. This study investigated the presence of Rickettsia spp. in ticks and ruminants in western of Iran by molecular methods. Materials and Methods: 250 blood samples were collected from sheep and goats, as well as 244 ticks were collected opportunistically from ruminants in the Kurdistan province. The collected samples were tested using a real-time quantitative PCR (qPCR) assay targeting the Rickettsia 16SrRNA gene. Rickettsia spp. positive by the qPCR were further amplified by conventional PCR of the gltA and OmpA genes. These ampliqons were further analyzed by sequencing. Results: The ticks species collected in this study included Rhipicephalus sanguineus, Rh. turanicus, Haemaphysalis concinna, and Dermacentor marginatus. In total, DNA of Rickettsia spp. was detected in 131 collected ticks (53.7%). Of the positives, Rickettsia slovaca (59.2%) and Ri. hoogstraalii (16.3%) were the most common species identified followed by Ri. raoultii, Ri. massiliae, Ri. sibirica, and Ri. conorii subsp. israelensis. In contrast, there were no positives observed in the blood samples collected from ruminants. Conclusion: The results indicate the presence of rickettsial species in ticks. The detection of these pathogens is significant because they cause clinical disease in humans. The results support the notion that the Iranian public health system needs to be more aware of these diseases.

History and Current Status of Mediterranean Spotted Fever (MSF) in the Crimean Peninsula and Neighboring Regions along the Black Sea Coast

Mediterranean spotted fever (MSF) is a tick-borne rickettsiosis caused by Rickettsia conorii subspecies conorii and transmitted to humans by Rhipicephalus sanguineus ticks. The disease was first discovered in Tunisia in 1910 and was subsequently reported from other Mediterranean countries. The first cases of MSF in the former Soviet Union were detected in 1936 on the Crimean Peninsula. This review summarizes the historic information and main features of MSF in that region and contemporary surveillance and control efforts for this rickettsiosis. Current data pertinent to the epidemiology of the disease, circulation of the ticks and distribution of animal hosts are discussed and compared for each of the countries in the Black Sea basin where MSF occurs.

Molecular surveillance for Rickettsia spp. and Bartonella spp. in ticks from Northern Iran

Tick-borne zoonotic diseases pose a threat to public health; hence, identifying the pathogenic agents associated with them is critical. The prevalence of Bartonella and Rickettsia in Iran is unknown. This study aimed to detect Rickettsia spp. and Bartonella species in ticks in northeast Iran and conduct phylogenetic analysis on these bacteria. Ticks from the sample bank in the Research Center for Emerging and Re-emerging Diseases were included in this study. The ticks were collected in 2017 and 2018 from domestic animals (sheep, goats, cows, camels, horses, dogs, and donkeys) and rodents in Golestan, Mazandaran, and Guilan provinces. Molecular methods were used to examine the DNA extracted from these samples to detect Rickettsia spp. and Bartonella species. The study examined a total of 3999 ticks. Ixodes ricinus (46.4%), Rhipicephalus turanicus (26.3%), and Rhipicephalus sanguineus (17.1%) were the most prevalent species. Among 638 DNA pools, real-time-PCR detected Rickettsia spp. in 161 (25.2%), mostly belonging to Rh. sanguineus (48.9%) and Rh. turanicus (41.9%). Golestan Province had the highest number of positive pools (29.7%). No positive samples for Bartonella were detected in a 638 pooled samples. Eight distinct Rickettsia species were detected in 65 sequenced samples, the majority of which were R. massiliae (n = 32, 49.2%) and R. sibirica (n = 20, 30.8%). Other species included R. rhipicephali (n = 3), R. aeschlimannii (n = 5), R. helvetica (n = 5), R. asiatica (n = 4), R. monacensis (n = 6), and R. raoultii (n = 1). The research findings may provide helpful information about tick-borne Rickettsiae in Iran and help to clarify the role of these arthropods in maintaining these agents. Rickettsia species were found to be circulating in three Northern provinces; thus, it is recommended that this disease be considered in the differential diagnosis of febrile diseases caused by tick bites and febrile diseases with skin rashes such as Crimean-Congo hemorrhagic fever (CCHF).

Investigation of Rickettsia conorii in Patients Suspected of Having Crimean-Congo Hemorrhagic Fever

Rickettsia conorii is the causative agent of Mediterranean spotted fever (MSF). Misdiagnosis of MSF may occur with febrile syndromes associated with rash and thrombocytopenia, such as Crimean-Congo hemorrhagic fever (CCHF). This study aimed to determine the prevalence of R. conorii among serum samples obtained from 260 suspected CCHF patients with features of MSF in Iran (2018–2020). The quantitative polymerase chain reaction (qPCR) method detected three (1.15%) positive 16S rDNA Rickettsia spp. samples that were classified as R. conorii subsp. conorii, R. conorii subsp. Israelensis, and R. helvetica using the sequencing of gltA, ompA, and 17kDa genes. Furthermore, R. conorii IgM antibodies presented in 38 (14.62%) patients by the enzyme-linked immunosorbent assay (ELISA) method. Out of 97 MSF patients with available paired serum samples, IgM seroconversion and a four-fold increase were observed in 14 (14.43%) and 12 (12.37%) patients, respectively. We concluded that rickettsial agents are present in Iran and may be misdiagnosed with other febrile syndromes.

Recent Advances in the Immunologic Method Applied to Tick-Borne Diseases in Brazil

Zoonotic-origin infectious diseases are one of the major concerns of human and veterinary health systems. Ticks, as vectors of several zoonotic diseases, are ranked second only to mosquitoes as vectors. Many ticks’ transmitted infections are still endemic in the Americas, Europe, and Africa and represent approximately 17% of their infectious diseases population. Although our scientific capacity to identify and diagnose diseases is increasing, it remains a challenge in the case of tick-borne conditions. For example, in 2017, 160 cases of the Brazilian Spotted Fever (BSF, a tick-borne illness) were confirmed, alarming the notifiable diseases information system. Conversely, Brazilian borreliosis and ehrlichiosis do not require notification. Still, an increasing number of cases in humans and dogs have been reported in southeast and northeastern Brazil. Immunological methods applied to human and dog tick-borne diseases (TBD) show low sensitivity and specificity, cross-reactions, and false IgM positivity. Thus, the diagnosis and management of TBD are hampered by the personal tools and indirect markers used. Therefore, specific and rapid methods urgently need to be developed to diagnose the various types of tick-borne bacterial diseases. This review presents a brief historical perspective on the evolution of serological assays and recent advances in diagnostic tests for TBD (ehrlichiosis, BSF, and borreliosis) in humans and dogs, mainly applied in Brazil. Additionally, this review covers the emerging technologies available in diagnosing TBD, including biosensors, and discusses their potential for future use as gold standards in diagnosing these diseases.

Rickettsia spp. in Rhipicephalus sanguineus sensu lato ticks collected from stray dogs in Kerman city, Iran

Rickettsial diseases are recognized as one of the most important vector-borne infectious diseases for humans all over the world. Dogs and their ticks are considered the most important reservoirs for Rickettsia spp., especially in spotted fever group rickettsioses. The aim of the study was to investigate Rickettsia infections in ticks collected from stray dogs in southeastern Iran. In this study, 50 stray dogs in Kerman city were randomly selected, of 68% and 52% of which were above 8 months age and male, respectively. Ticks were collected from the dog skins. After identification of collected ticks, genomic DNA of all ticks was extracted. DNA samples were tested using real-time PCR for Rickettsia spp. infections. The species of Rickettsia in positive samples were determined using gltA gene amplification and sequencing. A total of 250 ticks were collected from 50 stray dogs and all of them belonged to Rhipicephalus sanguineus sensu lato. Totally, 10 pooled of 50 pooled ticks were positive for Rickettsia spp. in real-time PCR and the minimal Rickettsial infection rate was 4% in this study. The identified Rickettsia spp. included R. massiliae (n = 5), R. rhipicephali (n = 1), and R. sibirica (n = 1). In this study, molecular evidence of Rickettsia spp. infection was observed in collected ticks from stray dogs in southeast Iran. More sensitivity to human and animal health care systems in southeastern Iran is essential to the diagnosis of suspected clinical cases that are related to rickettsiosis.

Genetic typing of isolates of Rickettsia typhi

Murine typhus, which is caused by Rickettsia typhi, has a wide range of clinical manifestations. It has a low mortality rate but may result in meningoencephalitis and interstitial pneumonia in severe cases. Comparisons of complete genome sequences of R. typhi isolates from North Carolina, USA (Wilmington), Myanmar (B9991PP), and Thailand (TH1527) identified only 26 single nucleotide polymorphism (SNP) and 7 insertion-deletion (INDEL) sites in these highly syntenic genomes. Assays were developed to further define the distribution of these variant sites among 15 additional isolates of R. typhi with different histories from Asia, the USA, and Africa. Mismatch amplification mutation assays (MAMA) were validated for 22 SNP sites, while the 7 INDEL sites were analyzed directly on agarose gels. Six SNP types, 9 INDEL types, 11 total types were identified among these 18 isolates. Replicate DNA samples as well as comparisons of isolates with different passage and source histories gave consistent genetic typing profiles. Comparison of the SNP and INDEL markers to R. typhi’s nearest neighbor Rickettsia prowazekii demonstrated that the majority of the SNPs represent intra-species variation that arose post divergence of these two species while several INDEL sites also exhibited intraspecies variability among the R. prowazekii genomes that have been completely sequenced. The assays for the presence of these SNP and INDEL sites, particularly the latter, comprise a low technology gel method for consistently distinguishing R. typhi and R. prowazekii as well as for differentiating genetic types of R. typhi.

Rickettsia typhi is an obligately intracellular bacterium which is most commonly transmitted by rat fleas to humans and can cause the disease murine (endemic) typhus wherever both humans and infected rats are present. However, this agent is also present in a variety of other arthropod species associated with other vertebrate animals. Its closest relative is Rickettsia prowazekii, the etiologic agent of epidemic typhus (human louse-borne) and sylvatic typhus (associated with flying squirrels and its ectoparasites in the Eastern United States). Both classic louse-borne and flea-borne typhus rickettsiae can cause fatal infections and have the potential for use as biothreat agents as they can be grown in large quantities. We investigated the genetic differences that can be found in different stocks of R. typhi. Our work is important for two reasons. We have developed robust and sensitive methods for distinguishing isolates of R. typhi originating from different continents; these new assays require only simple instrumentation which is available in nearly all biology laboratories. Our results also provided new insights confirming the probable origin of R. typhi in Asia and its likely cosmopolitan spread by rats on ships around the world.

Rickettsia conorii subsp. israelensis infection: a case report from southeast Iran

Background

Mediterranean spotted fever (MSF) is a zoonotic and vector-borne disease caused by Rickettsia conorii. We report a case (36 year-old-woman) of MSF caused by Rickettsia conorii from Iran.

Case presentation

In September 2019, the patient was admitted to the hospital in Kerman province with flu-like symptoms and maculopapular lesions. According to the laboratory results, thrombocytopenia, elevated liver enzymes, and cardiac enzymes were observed. Skin biopsy was examined for Crimean-Congo Hemorrhagic Fever (CCHF) and MSF using the Real-Time-PCR and ELISA method. Finally, the sample was positive for Rickettsia conorii subsp. israelensis and treated with doxycycline and completely recovered.

Conclusions

This study showed that MSF could be present in Iran. Therefore, identifying endemic areas in Iran for this disease should be on the agenda.

An Update on the Laboratory Diagnosis of Rickettsia spp. Infection

Rickettsia species causing human illness are present globally and can cause significant disease. Diagnosis and identification of this intracellular bacteria are challenging with many available diagnostic modalities suffering from several shortcomings. Detection of antibodies directed against Rickettsia spp. via serological methods remains widely used with a broad range of sensitivity and specificity values reported depending on the assay. Molecular methods, including polymerase chain reaction (PCR) testing, enables species-specific identification with a fast turnaround time; however, due to resource requirements, use in some endemic settings is limited. Reports on the use of next-generation sequencing (NGS) and metagenomics to diagnose Rickettsia spp. infection have been increasing. Despite offering several potential advantages in the diagnosis and surveillance of disease, genomic approaches are currently only limited to reference and research laboratories. Continued development of Rickettsia spp. diagnostics is required to improve disease detection and epidemiological surveillance, and to better understand transmission dynamics.

Current tools for the diagnosis and detection of spotted fever group Rickettsia

Spotted fever group (SFG) rickettsiae causes a number of diseases in humans worldwide, which can range from mild to highly lethal. Since the clinical presentations of rickettsioses caused by SFG rickettsiae are variable and may be similar to the diseases caused by other rickettsiae, such as Orientia tsutsugamushi (agent for scrub typhus), Coxiella burnetii (agent for Q fever) and the typhus group rickettsiae (agents for epidemic and murine typhus), the accurate diagnosis of infections caused by SFG Rickettsia remains challenging especially in resource-poor settings in developing countries. This review summarizes the various diagnostic and detection tools that are currently available for the confirmation of infections by SFG rickettsiae. The advantages and challenges pertaining to the different serological and molecular detections methods, as well as new assays in development, are discussed. The utility of the detection tools contributing to the surveillance of SFG rickettsiae in arthropods and animals are reviewed.

Searching and Finding the Hidden Treasure: A Retrospective Analysis of Rickettsial Disease Among Dutch International Travelers

BACKGROUND

Rickettsial disease (RD) is a prevalent and underestimated cause of febrile illness worldwide, especially in the absence of an inoculation eschar. We attempted to quantify this underestimation at our clinic, by investigating past cases of febrile illness in travelers who had tested negative for leptospirosis, a disease that can initially present similarly to non-eschar RD, and which we routinely consider when other important causes of unspecified febrile illness have tested negative.

METHODS

We performed a retrospective analysis in febrile returned travelers from Asia, Africa, or the Americas between 2010 and 2017, who had tested negative for leptospirosis. Serologic immunofluorescence assays were performed for Orientia tsutsugamushi (scrub typhus), typhus group, and spotted fever group RD. We performed a medical records review of all patients who tested positive. In case of a fitting medical history, cases were deemed either confirmed (based on convalescent serology) or suspected (based on single serology).

RESULTS

Among 97 patients, convalescent serology was available in 16 (16.5%) patients, and a single serology in 81 (83.5%) patients. RD was the likely diagnosis in 8 of 16 (50.0%) patients with convalescent serology, and in 8 of 81 (9.9%) with single serology. Of the 16 confirmed/suspected cases, 11 (69%) had been missed and 7 (44%) had not received adequate empiric antibiotic therapy.

CONCLUSIONS

This study shows that non-eschar RD is an important and poorly recognized cause of illness in travelers, even in a specialized travel clinic. A lower threshold to test and treat for RD is warranted in returning travelers with febrile illness.

Importation of Ticks on Companion Animals and the Risk of Spread of Tick-Borne Diseases to Non-Endemic Regions in Europe

Increased human mobility elevates the risk of exposure of companion animals travelling with their owners or imported from other regions to tick attacks. In this study, we highlight the potential role of dogs and cats taken for tourist trips or imported animals in the spread of ticks and tick-borne pathogens. The Rhipicephalus sanguineus tick, which is a vector of numerous pathogens causing diseases in animals and humans, is imported most frequently from endemic areas to many European countries. Additionally, alien tick species with high epizootic and epidemiological importance can be imported on dogs from other continents. Companion animals play an even greater role in the spread of autochthonous tick species and transmission of tick pathogens to other animals and humans. Although the veterinary and medical effects of the parasitism of ticks carried by companion animals travelling with owners or imported animals are poorly assessed, these animals seem to play a role in the rapid spread of tick-borne diseases. Development of strategies for protection of the health of companion animals in different geographic regions should take into account the potential emergence of unknown animal tick-borne diseases that can be transmitted by imported ticks.

New Real-Time PCRs to Differentiate Rickettsia spp. and Rickettsia conorii

Rickettsia species are an important cause of emerging infectious diseases in people and animals, and rickettsiosis is one of the oldest known vector-borne diseases. Laboratory diagnosis of Rickettsia is complex and time-consuming. This study was aimed at developing two quantitative real-time PCRs targeting ompB and ompA genes for the detection, respectively, of Rickettsia spp. and R. conorii DNA. Primers were designed following an analysis of Rickettsia gene sequences. The assays were optimized using SYBR Green and TaqMan methods and tested for sensitivity and specificity. This study allowed the development of powerful diagnostic methods, able to detect and quantify Rickettsia spp. DNA and differentiate R. conorii species.

Detection of Rickettsia Endosymbiont Bemisia Tabaci in the Amputated Limbs of Three Buerger's Disease Patients

Until recently, the aetiology of Buerger’s disease (BD) has been unknown. Although there is a close relationship between BD and smoking, it cannot explain the low prevalence of BD among smokers or the disease’s geographical distribution. Infectious pathogens, such as Rickettsial infection, have also been suggested as the trigger of BD development, but this theory has neither been proven nor ruled out. The aim of this study was to evaluate the footprint of Rickettsial infection in tissue specimens obtained from amputees with Buerger’s disease. Forty-nine tissue biopsies were obtained from three below-the-knee amputees who also had a diagnosis of BD according to Olin’s criteria (between 14–21 biopsies for each patient). After extraction of DNA from the tissue samples, the existence of 16srRNA was evaluated using a PCR test. The sequence of PCR products was evaluated using Geneious 11.1.2 software and NCBI blast. The 16srRNA was found in 3 to 7 samples from each patient. The sequence of the PCR products had a 98% homology with Rickettsia Tabaci. The sequences of the three patients were aligned, and no difference was found in the sequence of 16srRNA amongst the patients. Rickettsia Tabaci is a pathogen that infects tobacco leaves. Thus, BD might be an infectious disease for which smoking could be the route of pathogen entry into the bloodstreams of the sufferers. However, further studies are highly recommended to confirm this hypothesis.

Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles

The beetle genus Cephaloleia has evolved in association with tropical ginger plants and for many species their specific host plant associations are known. Here we show that the core microbiome of six closely related Costa Rican Cephaloleia species comprises only eight bacterial groups, including members of the Acinetobacter, Enterobacteriacea, Pseudomonas, Lactococcus, and Comamonas. The Acinetobacter and Enterobacteriacea together accounted for 35% of the total average 16S rRNA ribotypes recovered from all specimens. Further, microbiome diversity and community structure was significantly linked to beetle diet breadth, between those foraging on less than two plant types (specialists) versus over nine plant types (generalists). Moraxellaceae, Enterobacteriaceae, and Pseudomonadaceae were highly prevalent in specialist species, and also present in eggs, while Rickettsiaceae associated exclusively with generalist beetles. Bacteria isolated from Cephaloleia digestive systems had distinct capabilities and suggested a possible beneficial role in both digestion of plant-based compounds, including xylose, mannitol, and pectin, and possible detoxification, via lipases. Cephaloleia species are currently expanding their diets to include exotic invasive plants, yet it is unknown whether their microbial community plays a role in this transition. In this study, colonization of invasive plants was correlated with a dysbiosis of the microbiome, suggesting a possible relationship between gut bacteria and niche adaptation.

Ten years of R&D and full automation in molecular diagnosis

A 10-year experience of our automated molecular diagnostic platform that carries out 91 different real-time PCR is described. Progresses and future perspectives in molecular diagnostic microbiology are reviewed: why automation is important; how our platform was implemented; how homemade PCRs were developed; the advantages/disadvantages of homemade PCRs, including the critical aspects of troubleshooting and the need to further reduce the turnaround time for specific samples, at least for defined clinical settings such as emergencies. The future of molecular diagnosis depends on automation, and in a novel perspective, it is time now to fully acknowledge the true contribution of molecular diagnostic and to reconsider the indication for PCR, by also using these tests as first-line assays.

Comparative evaluation of two Rickettsia typhi-specific quantitative real-time PCRs for research and diagnostic purposes

Rickettsioses are caused by intracellular bacteria of the family of Rickettsiaceae. Rickettsia (R.) typhi is the causative agent of endemic typhus. The disease occurs worldwide and is one of the most prevalent rickettsioses. Rickettsial diseases, however, are generally underdiagnosed which is mainly due to the lack of sensitive and specific methods. In addition, methods for quantitative detection of the bacteria for research purposes are rare. We established two qPCRs for the detection of R. typhi by amplification of the outer membrane protein B (ompB) and parvulin-type PPIase (prsA) genes. Both qPCRs are specific and exclusively recognize R. typhi but no other rickettsiae including the closest relative, R. prowazekii. The prsA-based qPCR revealed to be much more sensitive than the amplification of ompB and provided highly reproducible results in the detection of R. typhi in organs of infected mice. Furthermore, as a nested PCR the prsA qPCR was applicable for the detection of R. typhi in human blood samples. Collectively, the prsA-based qPCR represents a reliable method for the quantitative detection of R. typhi for research purposes and is a promising candidate for differential diagnosis.

Usefulness of the early molecular diagnosis of Q fever and rickettsial diseases in patients with fever of intermediate duration

Most cases of fever of intermediate duration (FDI) in Spain are associated with infectious diseases (mainly Q fever and rickettsia infections). In clinical practice, the causal diagnosis of these entities is based on immunodiagnostic techniques, which are of little help in the early stages. Therefore, the aim of this study was to evaluate the usefulness of molecular techniques for the early diagnosis of Q fever and rickettsia diseases in patients with FDI. A PCR method was used to detect the presence of genetic material of Coxiella burnetii and Rickettsia spp. in blood specimens from 271 patients with FDI. The specificity of both techniques is high, allowing diagnosis in cases undiagnosed by specific antibodies detection. These data suggest that the use of molecular techniques, with proper selection of the study specimen, and using appropriate primers is a useful tool in the early diagnosis of the main causes of FDI, especially if serology is negative or inconclusive.

Molecular diagnosis of Rickettsia infection in patients from Tunisia

Diagnosis of rickettsioses had largely benefited from the development of molecular techniques. Unfortunately, in Tunisia, despite the large number of rickettsial cases registered every year, the Rickettsia species remain unidentified. In this study, we aimed to detect the Rickettsia species in clinical samples using molecular tests. A study was established to analyze skin biopsies, cutaneous swabs, and cerebrospinal fluid samples taken from clinically suspected patients to have rickettsial infection. Two molecular techniques were used to detect Rickettsia DNA: quantitative real time PCR (qPCR) and reverse line blot test (RLB). An analysis of the RLB hybridization assay results revealed the presence of Rickettsia DNA in skin biopsies (40.6%) and swabs (46.7%). Rickettsia conorii was the most prevalent identified species among tested samples. Other species of interest include Rickettsia typhi and Rickettsia massiliae. Using qPCR positivity rates in skin biopsies was 63.7% against 80% in swabs. R. conorii was the most frequently detected species, followed by R. typhi. The agreement between the two techniques was 68.6% (kappa=0.33). Molecular tests, especially using specific probes qPCR, allow for a rapid, better and confident diagnosis in clinical practice. They improve the survey of Mediterranean spotted fever which is considered to be the most important rickettsial infection in humans in Tunisia.

Strategies for detecting rickettsiae and diagnosing rickettsial diseases

Rickettsial diseases and scrub typhus constitute a group of the oldest known vector-borne diseases. The cosmopolitan distribution of the vectors that transmit rickettsiae and orientiae leads to a worldwide prevalence of these diseases. Despite their significant historical status, detection and diagnosis of these diseases are still evolving today. Serological methods remain among the most prevalent techniques used for the detection/diagnosis of rickettsial diseases and scrub typhus. Molecular techniques have been instrumental in increasing the sensitivity/specificity of diagnosis, identifying new Rickettsia and Orientia species and have enhanced epidemiological capabilities when used in combination with serological methods. In this review, we discuss these techniques and their associated pros and cons.

Development of Recombinase Polymerase Amplification Assays for Detection of Orientia tsutsugamushi or Rickettsia typhi

Sensitive, specific and rapid diagnostic tests for the detection of Orientia tsutsugamushi (O. tsutsugamushi) and Rickettsia typhi (R. typhi), the causative agents of scrub typhus and murine typhus, respectively, are necessary to accurately and promptly diagnose patients and ensure that they receive proper treatment. Recombinase polymerase amplification (RPA) assays using a lateral flow test (RPA-nfo) and real-time fluorescent detection (RPA-exo) were developed targeting the 47-kDa gene of O. tsutsugamushi or 17 kDa gene of R. typhi. The RPA assay was capable of detecting O. tsutsugamushi or R. typhi at levels comparable to that of the quantitative PCR method. Both the RPA-nfo and RPA-exo methods performed similarly with regards to sensitivity when detecting the 17 kDa gene of R. typhi. On the contrary, RPA-exo performed better than RPA-nfo in detecting the 47 kDa gene of O. tsutsugamushi. The clinical performance of the O. tsutsugamushi RPA assay was evaluated using either human patient samples or infected mouse samples. Eight out of ten PCR confirmed positives were determined positive by RPA, and all PCR confirmed negative samples were negative by RPA. Similar results were obtained for R. typhi spiked patient sera. The assays were able to differentiate O. tsutsugamushi and R. typhi from other phylogenetically related bacteria as well as mouse and human DNA. Furthermore, the RPA-nfo reaction was completed in 20 minutes at 37^oC followed by a 10 minute incubation at room temperature for development of an immunochromatographic strip. The RPA-exo reaction was completed in 20 minutes at 39^oC. The implementation of a cross contamination proof cassette to detect the RPA-nfo fluorescent amplicons provided an alternative to regular lateral flow detection strips, which are more prone to cross contamination. The RPA assays provide a highly time-efficient, sensitive and specific alternative to other methods for diagnosing scrub typhus or murine typhus.

Historically, rickettsial pathogens are among the leading causes of morbidity and mortality during military operations. Rickettsial diseases, lately, are reemerging in areas of known abundance or emerging in areas of unknown existence, posing a significant medical concern for local residents and travelers. The diseases are difficult to diagnose as they often share similar symptoms with many other diseases in the same geographical areas. Therefore, it is particularly challenging for clinicians to provide a timely and accurate diagnosis. A recombinase polymerase amplification (RPA)-based nucleic acid detection platform has been used to develop accurate, sensitive, specific, and easy-to-perform assays to detect O. tsutsugamushi or R. typhi, indicative of scrub typhus or murine typhus, respectively. These RPA assays provide similar limits of detection and specificity to that of qPCR. Unlike qPCR, they require no thermocycler and provide multiple end-point monitoring options amendable to different laboratory capabilities. This work presents an alternative assay platform for early detection of O. tsutsugamushi or R. typhi infection so that timely treatment can be prescribed in well-equipped laboratories as well as resource limited areas.

Comparison of two quantitative real time PCR assays for Rickettsia detection in patients from Tunisia

Background and objectives

Quantitative real time PCR (qPCR) offers rapid diagnosis of rickettsial infections. Thus, successful treatment could be initiated to avoid unfavorable outcome. Our aim was to compare two qPCR assays for Rickettsia detection and to evaluate their contribution in early diagnosis of rickettsial infection in Tunisian patients.

Patients and methods

Included patients were hospitalized in different hospitals in Tunisia from 2007 to 2012. Serology was performed by microimmunofluorescence assay using R. conorii and R. typhi antigens. Two duplex qPCRs, previously reported, were performed on collected skin biopsies and whole blood samples. The first duplex amplified all Rickettsia species (PanRick) and Rickettsia typhi DNA (Rtt). The second duplex detected spotted fever group Rickettsiae (RC00338) and typhus group Rickettsiae DNA (Rp278).

Results

Diagnosis of rickettsiosis was confirmed in 82 cases (57.7%). Among 44 skin biopsies obtained from patients with confirmed diagnosis, the first duplex was positive in 24 samples (54.5%), with three patients positive by Rtt qPCR. Using the second duplex, positivity was noted in 21 samples (47.7%), with two patients positive by Rp278 qPCR. Among79 whole blood samples obtained from patients with confirmed diagnosis, panRick qPCR was positive in 5 cases (6.3%) among which two were positive by Rtt qPCR. Using the second set of qPCRs, positivity was noted in four cases (5%) with one sample positive by Rp278 qPCR. Positivity rates of the two duplex qPCRs were significantly higher among patients presenting with negative first serum than those with already detectable antibodies.

Conclusions

Using qPCR offers a rapid diagnosis. The PanRick qPCR showed a higher sensitivity. Our study showed that this qPCR could offer a prompt diagnosis at the early stage of the disease. However, its implementation in routine needs cost/effectiveness evaluation.

Rickettsial diagnosis is challenging in routine laboratory. Serology offers only retrospective diagnosis. We aimed to introduce molecular methods in routine diagnosis of these infections. The lack of standardized methods led us to compare real time PCR assays previously reported in order to implement a clear strategies for diagnosis of these infections in our laboratory. Real time PCR proposed by Renvoisé et al includes two PCRs, one to detect spotted fever group and another to detect typhus group Rickettsiae. The real time PCR proposed by Giullieri et al includes a first PCR detecting 16rDNA of all Rickettsiae and if it is positive a second PCR detecting R. typhi should be performed. This second Real time PCR was shown to offer a slight higher sensitivity with a lower cost in our study. Skin biopsy specimens were more likely to show positive results than whole blood samples. Finally, positivity rates were higher among patients presenting at the first stage of the disease, essentially with negative serology.

MODERN APPROACHES TO LABORATORY DIAGNOSIS OF RICKETTSIAL DISEASES

Abstract. We present a concise review of contemporary laboratory methods for diagnosis of rickettsioses with special emphasis on diseases known in Russian Federation. Classic and emerging rickettsioses are transmitted by a diverse and expanding group of arthropod vectors including ticks, fleas, lice and mites. While epidemiological and clinical clues can provide information important for initial suspicion of rickettsial infection, sensitive and specific laboratory methods are necessary for providing probable or confirmed diagnosis of the rickettsial infection. Accurate and rapid confirmation of rickettsial infection is important for ensuring proper clinical care and prompt initiation of antibiotic therapy. Correct identification of the etiology of rickettsial diseases is also important for early identification of clustered cases, novel foci of infections, and for timely initiation of public health responses to these potentially fatal infections.

Real-time PCR as a diagnostic tool for bacterial diseases

In recent years, quantitative real-time PCR tests have been extensively developed in clinical microbiology laboratories for routine diagnosis of infectious diseases, particularly bacterial diseases. This molecular tool is well-suited for the rapid detection of bacteria directly in clinical specimens, allowing early, sensitive and specific laboratory confirmation of related diseases. It is particularly suitable for the diagnosis of infections caused by fastidious growth species, and the number of these pathogens has increased recently. This method also allows a rapid assessment of the presence of antibiotic resistance genes or gene mutations. Although this genetic approach is not always predictive of phenotypic resistances, in specific situations it may help to optimize the therapeutic management of patients. Finally, an approach combining the detection of pathogens, their mechanisms of antibiotic resistance, their virulence factors and bacterial load in clinical samples could lead to profound changes in the care of these infected patients.

Assessment of real-time PCR assay for detection of Rickettsia spp. and Rickettsia rickettsii in banked clinical samples

Two novel real-time PCR assays were developed for the detection of Rickettsia spp. One assay detects all tested Rickettsia spp.; the other is specific for Rickettsia rickettsii. Evaluation using DNA from human blood and tissue samples showed both assays to be more sensitive than nested PCR assays currently in use at the CDC.